Hi Saurabh,

Did you download the file again? You also can download old versions here: ftp://surfer.nmr.mgh.harvard.edu/pub/dist/freesurfer/

so we are sure that there is not anything missing in your freesurfer folder.

Can you write into the terminal: 

ls -l /usr/local/freesurfer

For your info: I get this:

~$ ls -l /usr/local/freesurfer
total 372
-rw-r--r--  1 root root  3302 May 14  2013 ASegStatsLUT.txt
-rw-r--r--  1 root root   728 May 14  2013 AUTHORS
drwxr-xr-x  7 root root  4096 May 14  2013 average
drwxr-xr-x  2 root root 32768 May 14  2013 bin
-rw-r--r--  1 root root    50 May 14  2013 build-stamp.txt
drwxr-xr-x  3 root root  4096 May 14  2013 data
-rw-r--r--  1 root root 47514 May 14  2013 DefectLUT.txt
drwxr-xr-x  3 root root  4096 May 14  2013 diffusion
drwxr-xr-x  3 root root  4096 May 14  2013 docs
-rw-r--r--  1 root root 84833 May 14  2013 FreeSurferColorLUT.txt
-rwxr-xr-x  1 root root 16760 May 14  2013 FreeSurferEnv.csh
-rwxr-xr-x  1 root root 16846 May 14  2013 FreeSurferEnv.sh
drwxr-xr-x  2 root root  4096 May 14  2013 fsafd
drwxr-xr-x  5 root root  4096 May 14  2013 fsfast
drwxr-xr-x 12 root root  4096 May 14  2013 lib
-rw-r--r--  1 root root 10297 May 14  2013 LICENSE
drwxr-xr-x  3 root root  4096 May 14  2013 matlab
drwxr-xr-x  9 root root  4096 Nov  1  2007 mni
-rw-r--r--  1 root root  4793 May 14  2013 NOTICE
-rw-r--r--  1 root root   635 May 14  2013 README
-rw-r--r--  1 root root 28445 May 14  2013 SegmentNoLUT.txt
drwxr-xr-x  2 root root  4096 May 14  2013 sessions
-rwxr-xr-x  1 root root  1352 May 14  2013 SetUpFreeSurfer.csh
-rwxr-xr-x  1 root root  1342 May 14  2013 SetUpFreeSurfer.sh
-rw-r--r--  1 root root  4104 May 14  2013 Simple_surface_labels2009.txt
drwxr-xr-x 15 root root  4096 Jan 28 16:24 subjects
-rw-r--r--  1 root root  1681 May 14  2013 tkmeditParcColorsCMA
drwxr-xr-x  2 root root  4096 May 14  2013 tktools
drwxr-xr-x 35 root root  4096 May 14  2013 trctrain
-rw-r--r--  1 root root    52 May 14  2013 VERSION
-rw-r--r--  1 root root 25944 May 14  2013 WMParcStatsLUT.txt

As you see there is also tktools.

What does it say if you type:

ls -l /usr/local/freesurfer/tktools/

This is my version:

~$ ls -l /usr/local/freesurfer/tktools/
total 93888
-rwxr-xr-x 1 root root    46572 May 14  2013 fsgdfPlot.tcl
-rw-r--r-- 1 root root     6180 May 14  2013 license.cortechs.txt
-rwxr-xr-x 1 root root    17992 May 14  2013 tkanalyse.tcl
-rwxr-xr-x 1 root root      722 May 14  2013 tkm_common.tcl
-rwxr-xr-x 1 root root     1591 May 14  2013 tkm_dialog.tcl
-rwxr-xr-x 1 root root      102 May 14  2013 tkmedit
-rwxr-xr-x 1 root root 25409422 May 14  2013 tkmedit.bin
-rwxr-xr-x 1 root root   154763 May 14  2013 tkmedit.tcl
-rwxr-xr-x 1 root root    40941 May 14  2013 tkm_functional.tcl
-rwxr-xr-x 1 root root     2805 May 14  2013 tkm_graph.tcl
-rwxr-xr-x 1 root root    47324 May 14  2013 tkm_wrappers.tcl
-rwxr-xr-x 1 root root      106 May 14  2013 tkregister
-rwxr-xr-x 1 root root      106 May 14  2013 tkregister2
-rwxr-xr-x 1 root root 22267238 May 14  2013 tkregister2.bin
-rwxr-xr-x 1 root root 22105890 May 14  2013 tkregister2_cmdl
-rwxr-xr-x 1 root root    27967 May 14  2013 tkregister2.tcl
-rwxr-xr-x 1 root root    27967 May 14  2013 tkregister.tcl
-rwxr-xr-x 1 root root      103 May 14  2013 tksurfer
-rwxr-xr-x 1 root root 25685088 May 14  2013 tksurfer.bin
-rwxr-xr-x 1 root root   200280 May 14  2013 tksurfer.tcl
-rwxr-xr-x 1 root root    56875 May 14  2013 tkUtils.tcl

Hope this helps,

M

2014-02-04 Saurabh Thakur <srbhthkr@gmail.com>:

Hi,

I am using laptop with 8Gb RAM,

i7 Core processor,

and

enough HDD....

still i m getting same erro ( /usr/local/freesurfer/tktools/tkmedit.bin: Command not found. ) because i m working on laptop...?

or

"recon-all --help " is working but tkmedit is not working

Hope to get response asap.

Thanks in advance.

Saurabh Thakur,

On Tue, Feb 4, 2014 at 2:09 PM, Markus Gschwind <markus.gschwind@gmail.com> wrote:

Hi Saurabh,

 

I recently installed FS un ubuntu 12.04, and it was not difficult.

 

I would recommend that you again download the file from here

http://surfer.nmr.mgh.harvard.edu/fswiki/Download (I took the Centos4 file)

 

to make sure that it is complete.

 

Than you "untar" the file at any given place (most people recomment /usr/local/ but you need to do it in "sudo" mode).

 

Then make sure that you put the license file at the right place (http://surfer.nmr.mgh.harvard.edu/fswiki/LinuxInstall)

 

and adapt the configuration file (http://surfer.nmr.mgh.harvard.edu/fswiki/SetupConfiguration)

 

I used bash and it worked well.

 

Take care that you have writing permission on the folders you want to use ($SUBJECT_DIR).

For that reason I copied the folder "bert" to my home folder in order to be able to run the installation test as recommended here: http://surfer.nmr.mgh.harvard.edu/fswiki/TestingFreeSurfer

 

Hope that helps!

Cheers,

Markus

2014-02-04 Saurabh Thakur <srbhthkr@gmail.com>:

Hello everyone,

Can u anyone help me in simplest and best way to install freesurfer on

i m not able to run command :
1. tkmedit
2. tksurfer.

System specification:

Dell laptop
Ubuntu 12.04 LTS

RAM 8Gb

Graphics cards: Nvidia cards 1 Gb

Thanks in advance.

Saurabh Thakur,

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